Package Bio :: Package Gobase
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Package Gobase

source code

This module provides code to work with files from Gobase. http://megasun.bch.umontreal.ca/gobase/

Classes: Record Holds gobase sequence data. Iterator Iterates over sequence data in a gobase file. Dictionary Accesses a gobase file using a dictionary interface. RecordParser Parses gobase sequence data into a Record object.

_Scanner Scans a gobase-format stream. _RecordConsumer Consumes gobase data to a Record object.

Functions: index_file Index a FASTA file for a Dictionary.

Classes [hide private]
  Record
Holds information from a Gobase record.
  SequenceRecord
Holds information from a Gobase record.
  GeneRecord
Holds information from a Gobase record.
  ProteinRecord
Holds information from a Gobase record.
  Iterator
Returns one record at a time from a Gobase file.
  Dictionary
Accesses a gobase file using a dictionary interface.
  RecordParser
Parses Gobase sequence data into a Record object.
  _Scanner
Scans a gobase file.
  _RecordConsumer
Consumer that converts a gobase record to a Record object.
Functions [hide private]
 
index_file(filename, indexname, rec2key=None)
index_file(filename, ind/exname, rec2key=None)
source code
Variables [hide private]
  __warningregistry__ = {('Bio.Gobase is deprecated, as this mod...
  xml_support = 1
Function Details [hide private]

index_file(filename, indexname, rec2key=None)

source code 

index_file(filename, ind/exname, rec2key=None)

Index a gobase file. filename is the name of the file. indexname is the name of the dictionary. rec2key is an optional callback that takes a Record and generates a unique key (e.g. the accession number) for the record. If not specified, the sequence title will be used.


Variables Details [hide private]

__warningregistry__

Value:
{('Bio.Gobase is deprecated, as this module doesn\'t seem to have any \
users. If you are using Bio.Gobase, please get in contact with the Bio\
python developers at biopython-dev@biopython.org to avoid permanent re\
moval of this module.',
  <type 'exceptions.DeprecationWarning'>,
  27): 1}